Hey, I'm looking to add a similar mod with settings for Transport Drones so supply depots can have larger item buffers. Any chance I can get access to your source for this? Or alternatively, would you mind giving me some pointers? Am a bit stuck on how to change another mod's settings from my mod, and by the looks of it, you pulled that off.

Source? You can just look in the game file, Lua does not need to be compiled by modders.

Transport Drones supply depot is a chest, you can simply increase the inventory size by changing the inventory_size in its prototype. A one line like this should work:
data.raw.container["supply-depot-chest"].container_size = 500
or replace the 500 with a value from a startup setting, if you can manage to find out how to do that.